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Ponnimbaduge Perera P, Perez Guerra D, Riddle MR. The Mexican Tetra, Astyanax mexicanus, as a Model System in Cell and Developmental Biology. Annu Rev Cell Dev Biol 2023; 39:23-44. [PMID: 37437210 DOI: 10.1146/annurev-cellbio-012023-014003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Our understanding of cell and developmental biology has been greatly aided by a focus on a small number of model organisms. However, we are now in an era where techniques to investigate gene function can be applied across phyla, allowing scientists to explore the diversity and flexibility of developmental mechanisms and gain a deeper understanding of life. Researchers comparing the eyeless cave-adapted Mexican tetra, Astyanax mexicanus, with its river-dwelling counterpart are revealing how the development of the eyes, pigment, brain, cranium, blood, and digestive system evolves as animals adapt to new environments. Breakthroughs in our understanding of the genetic and developmental basis of regressive and constructive trait evolution have come from A. mexicanus research. They include understanding the types of mutations that alter traits, which cellular and developmental processes they affect, and how they lead to pleiotropy. We review recent progress in the field and highlight areas for future investigations that include evolution of sex differentiation, neural crest development, and metabolic regulation of embryogenesis.
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Affiliation(s)
| | | | - Misty R Riddle
- Department of Biology, University of Nevada, Reno, Nevada, USA;
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2
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De Falco A, Iolascon A, Ascione F, Piscopo C. New Insights in 9q21.13 Microdeletion Syndrome: Genotype-Phenotype Correlation of 28 Patients. Genes (Basel) 2023; 14:genes14051116. [PMID: 37239476 DOI: 10.3390/genes14051116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The implementation of array comparative genomic hybridisation (array-CGH) allows us to describe new microdeletion/microduplication syndromes which were previously not identified. 9q21.13 microdeletion syndrome is a genetic condition due to the loss of a critical genomic region of approximately 750kb and includes several genes, such as RORB and TRPM6. Here, we report a case of a 7-year-old boy affected by 9q21.13 microdeletion syndrome. He presents with global developmental delay, intellectual disability, autistic behaviour, seizures and facial dysmorphism. Moreover, he has severe myopia, which was previously reported in only another patient with 9q21.13 deletion, and brain anomalies which were never described before in 9q21.13 microdeletion syndrome. We also collect 17 patients from a literature search and 10 cases from DECIPHER database with a total number of 28 patients (including our case). In order to better investigate the four candidate genes RORB, TRPM6, PCSK5, and PRUNE2 for neurological phenotype, we make, for the first time, a classification in four groups of all the collected 28 patients. This classification is based both on the genomic position of the deletions included in the 9q21.3 locus deleted in our patient and on the different involvement of the four-candidate gene. In this way, we compare the clinical problems, the radiological findings, and the dysmorphic features of each group and of all the 28 patients in our article. Moreover, we perform the genotype-phenotype correlation of the 28 patients to better define the syndromic spectrum of 9q21.13 microdeletion syndrome. Finally, we propose a baseline ophthalmological and neurological monitoring of this syndrome.
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Affiliation(s)
- Alessandro De Falco
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare di Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy
| | - Achille Iolascon
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare di Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Flora Ascione
- Hospital Directorate, A.O.R.N. "Antonio Cardarelli", 80100 Naples, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. "Antonio Cardarelli", 80100 Naples, Italy
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3
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Characterization of biklf/klf17-deficient zebrafish in posterior lateral line neuromast and hatching gland development. Sci Rep 2019; 9:13680. [PMID: 31558744 PMCID: PMC6763433 DOI: 10.1038/s41598-019-50149-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/29/2019] [Indexed: 11/08/2022] Open
Abstract
Krüpple-like factors (Klfs) are highly conserved zinc-finger transcription factors that regulate various developmental processes, such as haematopoiesis and cardiovascular development. In zebrafish, transient knockdown analysis of biklf/klf17 using antisense morpholino suggests the involvement of biklf/klf17 in primitive erythropoiesis and hatching gland development; however, the continuous physiological importance of klf17 remains uncharacterized under the genetic ablation of the klf17 gene among vertebrates. We established the klf17-disrupted zebrafish lines using the CRISPR/Cas9 technology and performed phenotypic analysis throughout early embryogenesis. We found that the klf17-deficient embryos exhibited abnormal lateral line neuromast deposition, whereas the production of primitive erythrocytes and haemoglobin production were observed in the klf17-deficient embryos. The expression of lateral line neuromast genes, klf17 and s100t, in the klf17-deficient embryos was detected in posterior lateral line neuromasts abnormally positioned at short intervals. Furthermore, the klf17-deficient embryos failed to hatch and died without hatching around 15 days post-fertilization (dpf), whereas the dechorionated klf17-deficient embryos and wild-type embryos were alive at 15 dpf. The klf17-deficient embryos abolished hatching gland cells and Ctsl1b protein expression, and eliminated the expression of polster and hatching gland marker genes, he1.1, ctsl1b and cd63. Thus, the klf17 gene plays important roles in posterior lateral line neuromast and hatching gland development.
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4
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Rieder JM, Vonlanthen P, Seehausen O, Lucek K. Allopatric and sympatric diversification within roach (Rutilus rutilus) of large pre-alpine lakes. J Evol Biol 2019; 32:1174-1185. [PMID: 31257688 DOI: 10.1111/jeb.13502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/14/2019] [Accepted: 06/19/2019] [Indexed: 12/19/2022]
Abstract
Intraspecific differentiation in response to divergent natural selection between environments is a common phenomenon in some northern freshwater fishes, especially salmonids and stickleback. Understanding why these taxa diversify and undergo adaptive radiations while most other fish species in the same environments do not, remains an open question. The possibility for intraspecific diversification has rarely been evaluated for most northern freshwater fish species. Here, we assess the potential for intraspecific differentiation between and within lake populations of roach (Rutilus rutilus)-a widespread and abundant cyprinid species-in lakes in which salmonids have evolved endemic adaptive radiations. Based on more than 3,000 polymorphic RADseq markers, we detected low but significant genetic differentiation between roach populations of two ultraoligotrophic lakes and between these and populations from other lakes. This, together with differentiation in head morphology and stable isotope signatures, suggests evolutionary and ecological differentiation among some of our studied populations. Next, we tested for intralacustrine diversification of roach within Lake Brienz, the most pristine lake surveyed in this study. We found significant phenotypic evidence for ecological intralacustrine differentiation between roach caught over a muddy substrate and those caught over a rocky substrate. However, evidence for intralacustrine genetic differentiation is at best subtle and phenotypic changes may therefore be mostly plastic. Overall, our findings suggest roach can differ between ecologically distinct lakes, but the extent of intralacustrine ecological differentiation is weak, which contrasts with the strong differentiation among endemic species of whitefish in the same lakes.
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Affiliation(s)
- Jessica M Rieder
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology and Evolution, Center of Ecology, Evolution, and Biogeochemistry, Kastanienbaum, Switzerland.,Centre for Fish and Wildlife Health, Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Pascal Vonlanthen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology and Evolution, Center of Ecology, Evolution, and Biogeochemistry, Kastanienbaum, Switzerland.,Aquabios GmbH, Cordast, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology and Evolution, Center of Ecology, Evolution, and Biogeochemistry, Kastanienbaum, Switzerland
| | - Kay Lucek
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology and Evolution, Center of Ecology, Evolution, and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Environmental Sciences, University of Basel, Basel, Switzerland
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5
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Rare Case of a Heterozygous Microdeletion 9q21.11-q21.2: Clinical and Genetic Characteristics. Balkan J Med Genet 2019; 21:59-62. [PMID: 30984527 PMCID: PMC6454245 DOI: 10.2478/bjmg-2018-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Intellectual disability is affecting 3.0-4.0% of the general population. Copy number variants (CNVs) are a significant cause leading to neurodevelopmental disorders such as intellectual disability, epilepsy, autism spectrum disorders and developmental delay. The use of single nucleotide polymorphism (SNP)-array and array comparative genomic hybridization (aCGH) as diagnostic tools has led to the recognition of new microdeletion/microduplication syndromes associated with neurodevelopmental disorders. It is also useful for further characterization of marker chromosomes. Here, we report a girl with mild intellectual disability and mild facial dysmorphisms. Cytogenetic analysis showed a marker chromosome in some percent of the cells and was followed by SNP-array karyotyping that detected, in addition, a 9655 Mb de novo interstitial deletion at 9q21.1-9q21.2.
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6
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Application of Zebrafish and Knockdown Technology to Define Progranulin Neuronal Function. Methods Mol Biol 2019; 1806:207-231. [PMID: 29956279 DOI: 10.1007/978-1-4939-8559-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The zebrafish (Danio rerio), a small tropical fish, has become a powerful model for the study of early vertebrate development, human diseases, and drug screening. Zebrafish provides large numbers of optically clear embryos, and its development is very rapid. Overexpression or under-expression of proteins can be effectively achieved by microinjection of mRNA or morpholino antisense oligonucleotides (MOs), respectively, into developing embryos at the 1-2 cell stage. The function of a particular protein can be revealed by correlating gene expression patterns with the phenotypes observed from over- or under-expression. We defined the expression pattern of zebrafish progranulin A (zfPGRN-A), an orthologue to the single human PGRN by whole-mount in situ hybridization (ISH) and immunofluorescence (IF). The MO-mediated knockdown of zfPGRN-A expression generated embryos that display abnormal motor neuron development resulting in touch-evoked swimming deficits.
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7
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Brander SM, Jeffries KM, Cole BJ, DeCourten BM, White JW, Hasenbein S, Fangue NA, Connon RE. Transcriptomic changes underlie altered egg protein production and reduced fecundity in an estuarine model fish exposed to bifenthrin. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 174:247-60. [PMID: 26975043 DOI: 10.1016/j.aquatox.2016.02.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/15/2016] [Accepted: 02/18/2016] [Indexed: 05/15/2023]
Abstract
Pyrethroid pesticides are a class of insecticides found to have endocrine disrupting properties in vertebrates such as fishes and in human cell lines. Endocrine disrupting chemicals (EDCs) are environmental contaminants that mimic or alter the process of hormone signaling. In particular, EDCs that alter estrogen and androgen signaling pathways are of major concern for fishes because these EDCs may alter reproductive physiology, behavior, and ultimately sex ratio. Bifenthrin, a pyrethroid with escalating usage, is confirmed to disrupt estrogen signaling in several species of fish, including Menidia beryllina (inland silverside), an Atherinid recently established as a euryhaline model. Our main objective was to broadly assess the molecular and physiological responses of M. beryllina to the ng/L concentrations of bifenthrin typically found in the environment, with a focus on endocrine-related effects, and to discern links between different tiers of the biological hierarchy. As such, we evaluated the response of juvenile Menidia to bifenthrin using a Menidia-specific microarray, quantitative real-time polymerase chain reaction (qPCR) on specific endocrine-related genes of interest, and a Menidia-specific ELISA to the egg-coat protein choriogenin, to evaluate a multitude of molecular-level responses that would inform mechanisms of toxicity and any underlying causes of change at higher biological levels of organization. The sublethal nominal concentrations tested (0.5, 5 and 50ng/L) were chosen to represent the range of concentrations observed in the environment and to provide coverage of a variety of potential responses. We then employed a 21-day reproductive assay to evaluate reproductive responses to bifenthrin (at 0.5ng/L) in a separate group of adult M. beryllina. The microarray analysis indicated that bifenthrin influences a diverse suite of molecular pathways, from baseline metabolic processes to carcinogenesis. A more targeted examination of gene expression via qPCR demonstrated that bifenthrin downregulates a number of estrogen-related transcripts, particularly at the lowest exposure level. Choriogenin protein also decreased with exposure to increasing concentrations of bifenthrin, and adult M. beryllina exposed to 0.5ng/L had significantly reduced reproductive output (fertilized eggs per female). This reduction in fecundity is consistent with observed changes in endocrine-related gene expression and choriogenin production. Taken together, our results demonstrate that environmental concentrations of bifenthrin have potential to interfere with metabolic processes, endocrine signaling, and to decrease reproductive output.
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Affiliation(s)
- Susanne M Brander
- Biology & Marine Biology, University of North Carolina, Wilmington, 601 South College Road, Wilmington, NC 28403, United States.
| | - Ken M Jeffries
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Bryan J Cole
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Bethany M DeCourten
- Biology & Marine Biology, University of North Carolina, Wilmington, 601 South College Road, Wilmington, NC 28403, United States
| | - J Wilson White
- Biology & Marine Biology, University of North Carolina, Wilmington, 601 South College Road, Wilmington, NC 28403, United States
| | - Simone Hasenbein
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Nann A Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Richard E Connon
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
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8
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Erickson T, Nicolson T. Identification of sensory hair-cell transcripts by thiouracil-tagging in zebrafish. BMC Genomics 2015; 16:842. [PMID: 26494580 PMCID: PMC4619078 DOI: 10.1186/s12864-015-2072-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/13/2015] [Indexed: 12/13/2022] Open
Abstract
Background Sensory hair cells are exquisitely sensitive to mechanical stimuli and as such, are prone to damage and apoptosis during dissections or in vitro manipulations. Thiouracil (TU)-tagging is a noninvasive method to label cell type-specific transcripts in an intact organism, thereby meeting the challenge of how to analyze gene expression in hair cells without the need to sort cells. We adapted TU-tagging to zebrafish to identify novel transcripts expressed in the sensory hair cells of the developing acoustico-lateralis organs. Methods We created a transgenic line of zebrafish expressing the T.gondii uracil phospho-ribosyltransferase (UPRT) enzyme specifically in the hair cells of the inner ear and lateral line organ. RNA was labeled by exposing 3 days post-fertilization (dpf) UPRT transgenic larvae to 2.5 mM 4-thiouracil (4TU) for 15 hours. Following total RNA isolation, poly(A) mRNA enrichment, and purification of TU-tagged RNA, deep sequencing was performed on the input and TU-tagged RNA samples. Results Analysis of the RNA sequencing data revealed the expression of 28 transcripts that were significantly enriched (adjusted p-value < 0.05) in the UPRT TU-tagged RNA relative to the input sample. Of the 25 TU-tagged transcripts with mammalian homologs, the expression of 18 had not been previously demonstrated in zebrafish hair cells. The hair cell-restricted expression for 17 of these transcripts was confirmed by whole mount mRNA in situ hybridization in 3 dpf larvae. Conclusions The hair cell-restricted pattern of expression of these genes offers insight into the biology of this receptor cell type and may serve as useful markers to study the development and function of sensory hair cells. In addition, our study demonstrates the utility of TU-tagging to study nascent transcripts in specific cell types that are relatively rare in the context of the whole zebrafish larvae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2072-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Timothy Erickson
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
| | - Teresa Nicolson
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
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Yoshizawa M, Robinson BG, Duboué ER, Masek P, Jaggard JB, O'Quin KE, Borowsky RL, Jeffery WR, Keene AC. Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish. BMC Biol 2015; 13:15. [PMID: 25761998 PMCID: PMC4364459 DOI: 10.1186/s12915-015-0119-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sleep is characterized by extended periods of quiescence and reduced responsiveness to sensory stimuli. Animals ranging from insects to mammals adapt to environments with limited food by suppressing sleep and enhancing their response to food cues, yet little is known about the genetic and evolutionary relationship between these processes. The blind Mexican cavefish, Astyanax mexicanus is a powerful model for elucidating the genetic mechanisms underlying behavioral evolution. A. mexicanus comprises an extant ancestral-type surface dwelling morph and at least five independently evolved cave populations. Evolutionary convergence on sleep loss and vibration attraction behavior, which is involved in prey seeking, have been documented in cavefish raising the possibility that enhanced sensory responsiveness underlies changes in sleep. RESULTS We established a system to study sleep and vibration attraction behavior in adult A. mexicanus and used high coverage quantitative trait loci (QTL) mapping to investigate the functional and evolutionary relationship between these traits. Analysis of surface-cave F2 hybrid fish and an outbred cave population indicates that independent genetic factors underlie changes in sleep/locomotor activity and vibration attraction behavior. High-coverage QTL mapping with genotyping-by-sequencing technology identify two novel QTL intervals that associate with locomotor activity and include the narcolepsy-associated tp53 regulating kinase. These QTLs represent the first genomic localization of locomotor activity in cavefish and are distinct from two QTLs previously identified as associating with vibration attraction behavior. CONCLUSIONS Taken together, these results localize genomic regions underlying sleep/locomotor and sensory changes in cavefish populations and provide evidence that sleep loss evolved independently from enhanced sensory responsiveness.
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Affiliation(s)
- Masato Yoshizawa
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA. .,Department of Biology, University of Hawaii, Manoa, Honolulu, HI, 96822, USA.
| | - Beatriz G Robinson
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Erik R Duboué
- Department of Biology, New York University, New York, NY, 10012, USA. .,Present address: Carnegie Institution for Science, Department of Embryology, Baltimore, MD, 21218, USA.
| | - Pavel Masek
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - James B Jaggard
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Kelly E O'Quin
- Department of Biology, Centre College, Danville, KY, 40422, USA.
| | | | - William R Jeffery
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Alex C Keene
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
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10
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Common DNA variants predict tall stature in Europeans. Hum Genet 2013; 133:587-97. [DOI: 10.1007/s00439-013-1394-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/03/2013] [Indexed: 12/14/2022]
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11
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Chitramuthu BP, Bennett HPJ. High resolution whole mount in situ hybridization within zebrafish embryos to study gene expression and function. J Vis Exp 2013:e50644. [PMID: 24192694 PMCID: PMC4396715 DOI: 10.3791/50644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
This article focuses on whole-mount in situ hybridization (WISH) of zebrafish embryos. The WISH technology facilitates the assessment of gene expression both in terms of tissue distribution and developmental stage. Protocols are described for the use of WISH of zebrafish embryos using antisense RNA probes labeled with digoxigenin. Probes are generated by incorporating digoxigenin-linked nucleotides through in vitro transcription of gene templates that have been cloned and linearized. The chorions of embryos harvested at defined developmental stages are removed before incubation with specific probes. Following a washing procedure to remove excess probe, embryos are incubated with anti-digoxigenin antibody conjugated with alkaline phosphatase. By employing a chromogenic substrate for alkaline phosphatase, specific gene expression can be assessed. Depending on the level of gene expression the entire procedure can be completed within 2-3 days.
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12
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Boudry-Labis E, Demeer B, Le Caignec C, Isidor B, Mathieu-Dramard M, Plessis G, George AM, Taylor J, Aftimos S, Wiemer-Kruel A, Kohlhase J, Annerén G, Firth H, Simonic I, Vermeesch J, Thuresson AC, Copin H, Love DR, Andrieux J. A novel microdeletion syndrome at 9q21.13 characterised by mental retardation, speech delay, epilepsy and characteristic facial features. Eur J Med Genet 2012; 56:163-70. [PMID: 23279911 DOI: 10.1016/j.ejmg.2012.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 12/17/2012] [Indexed: 11/29/2022]
Abstract
The increased use of array-CGH and SNP-arrays for genetic diagnosis has led to the identification of new microdeletion/microduplication syndromes and enabled genotype-phenotype correlations to be made. In this study, nine patients with 9q21 deletions were investigated and compared with four previously Decipher reported patients. Genotype-phenotype comparisons of 13 patients revealed several common major characteristics including significant developmental delay, epilepsy, neuro-behavioural disorders and recognizable facial features including hypertelorism, feature-less philtrum, and a thin upper lip. The molecular investigation identified deletions with different breakpoints and of variable lengths, but the 750 kb smallest overlapping deleted region includes four genes. Among these genes, RORB is a strong candidate for a neurological phenotype. To our knowledge, this is the first published report of 9q21 microdeletions and our observations strongly suggest that these deletions are responsible for a new genetic syndrome characterised by mental retardation with speech delay, epilepsy, autistic behaviour and moderate facial dysmorphy.
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Affiliation(s)
- Elise Boudry-Labis
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHRU de Lille, Avenue Eugène Avinée, 59037 Lille, France.
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Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. ZEITSCHRIFT FUR ANGEWANDTE ICHTHYOLOGIE = JOURNAL OF APPLIED ICHTHYOLOGY 2012; 28:300-305. [PMID: 22736877 PMCID: PMC3377363 DOI: 10.1111/j.1439-0426.2012.01985.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 03/08/2012] [Indexed: 05/02/2023]
Abstract
The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2,500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery.
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Affiliation(s)
- By Paula Mabee
- Department of Biology, 414 East Clark Street, University of South Dakota, Vermillion, South Dakota, United States of America
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Abstract
The Zebrafish (Danio rerio) is a powerful and well-established tool used extensively for the study of early vertebrate development and as a model of human diseases. Zebrafish genes orthologous to their mammalian counterparts generally share conserved biological function. Protein knockdown or overexpression can be effectively achieved by microinjection of morpholino antisense oligonucleotides (MOs) or mRNA, respectively, into developing embryos at the one- to two-cell stage. Correlating gene expression patterns with the characterizing of phenotypes resulting from over- or underexpression can reveal the function of a particular protein. The microinjection technique is simple and results are reproducible. We defined the expression pattern of the proprotein convertase PCSK5 within the lateral line neuromasts and various organs including the liver, gut and otic vesicle by whole-mount in situ hybridization (ISH) and immunofluorescence (IF). MO-mediated knockdown of zebrafish PCSK5 expression generated embryos that display abnormal neuromast deposition within the lateral line system resulting in uncoordinated patterns of swimming.
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Couture F, D'Anjou F, Day R. On the cutting edge of proprotein convertase pharmacology: from molecular concepts to clinical applications. Biomol Concepts 2011; 2:421-438. [PMID: 22308173 DOI: 10.1515/bmc.2011.034] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
There is increasing interest in the therapeutic targeting of proteases for the treatment of important diseases. Additionally new protein-based therapeutic strategies have the potential to widen the available treatments against these pathologies. In the last decade, accumulated evidence has confirmed that the family of proteases known as proprotein convertases (PCs) are potential targets for viral infections, osteoarthritis, cancer and cardiovascular disease, among others. Nevertheless, there are still many unanswered questions about the relevance of targeting PCs in a therapeutic context, especially regarding the anticipated secondary effects of treatment, considering the observed embryonic lethality of some PC knockout mice. In this review, the benefits of PCs as pharmacological targets will be discussed, with focus on concepts and strategies, as well as on the state of advancement of actual and future inhibitors.
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Affiliation(s)
- Frédéric Couture
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke J1H 5N4, Québec, Canada
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